                      :-) GROMACS - gmx mdrun, 2019.6 (-:

                            GROMACS is written by:
     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    
 Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     
  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  
  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    
  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   
    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   
    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  
   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen 
 Christian Wennberg    Maarten Wolf   
                           and the project leaders:
        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2018, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:      gmx mdrun, version 2019.6
Executable:   /usr/bin/gmx
Data prefix:  /usr
Working dir:  /mnt/3wd5-rs2/313k
Process ID:   140425
Command line:
  gmx mdrun -deffnm md_1_20 -cpi md_0_10.cpt -noappend -v

GROMACS version:    2019.6
Precision:          single
Memory model:       64 bit
MPI library:        thread_mpi
OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 64)
GPU support:        OpenCL
SIMD instructions:  SSE2
FFT library:        fftw-3.3.5-sse2-avx
RDTSCP usage:       disabled
TNG support:        enabled
Hwloc support:      hwloc-2.2.0
Tracing support:    disabled
C compiler:         /usr/bin/cc GNU 8.4.1
C compiler flags:    -msse2   -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -DNDEBUG -funroll-all-loops -fexcess-precision=fast  
C++ compiler:       /usr/bin/c++ GNU 8.4.1
C++ compiler flags:  -msse2   -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11   -DNDEBUG -funroll-all-loops -fexcess-precision=fast  
OpenCL include dir: /usr/include
OpenCL library:     /usr/lib64/libOpenCL.so
OpenCL version:     2.2

NOTE: Detection of GPUs failed. The API reported:
      No valid OpenCL driver found
      GROMACS cannot run tasks on a GPU.

Running on 1 node with total 128 cores, 256 logical cores, 0 compatible GPUs
Hardware detected:
  CPU info:
    Vendor: AMD
    Brand:  AMD EPYC 7J13 64-Core Processor                
    Family: 25   Model: 1   Stepping: 1
    Features: aes amd apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt lahf misalignsse mmx msr nonstop_tsc pcid pclmuldq pdpe1gb popcnt pse rdrnd rdtscp sha sse2 sse3 sse4a sse4.1 sse4.2 ssse3 x2apic
  Hardware topology: Full, with devices
    Sockets, cores, and logical processors:
      Socket  0: [   0 128] [   1 129] [   2 130] [   3 131] [   4 132] [   5 133] [   6 134] [   7 135] [   8 136] [   9 137] [  10 138] [  11 139] [  12 140] [  13 141] [  14 142] [  15 143] [  16 144] [  17 145] [  18 146] [  19 147] [  20 148] [  21 149] [  22 150] [  23 151] [  24 152] [  25 153] [  26 154] [  27 155] [  28 156] [  29 157] [  30 158] [  31 159] [  32 160] [  33 161] [  34 162] [  35 163] [  36 164] [  37 165] [  38 166] [  39 167] [  40 168] [  41 169] [  42 170] [  43 171] [  44 172] [  45 173] [  46 174] [  47 175] [  48 176] [  49 177] [  50 178] [  51 179] [  52 180] [  53 181] [  54 182] [  55 183] [  56 184] [  57 185] [  58 186] [  59 187] [  60 188] [  61 189] [  62 190] [  63 191]
      Socket  1: [  64 192] [  65 193] [  66 194] [  67 195] [  68 196] [  69 197] [  70 198] [  71 199] [  72 200] [  73 201] [  74 202] [  75 203] [  76 204] [  77 205] [  78 206] [  79 207] [  80 208] [  81 209] [  82 210] [  83 211] [  84 212] [  85 213] [  86 214] [  87 215] [  88 216] [  89 217] [  90 218] [  91 219] [  92 220] [  93 221] [  94 222] [  95 223] [  96 224] [  97 225] [  98 226] [  99 227] [ 100 228] [ 101 229] [ 102 230] [ 103 231] [ 104 232] [ 105 233] [ 106 234] [ 107 235] [ 108 236] [ 109 237] [ 110 238] [ 111 239] [ 112 240] [ 113 241] [ 114 242] [ 115 243] [ 116 244] [ 117 245] [ 118 246] [ 119 247] [ 120 248] [ 121 249] [ 122 250] [ 123 251] [ 124 252] [ 125 253] [ 126 254] [ 127 255]
    Numa nodes:
      Node  0 (1068870516736 bytes mem):   0 128   1 129   2 130   3 131   4 132   5 133   6 134   7 135   8 136   9 137  10 138  11 139  12 140  13 141  14 142  15 143  16 144  17 145  18 146  19 147  20 148  21 149  22 150  23 151  24 152  25 153  26 154  27 155  28 156  29 157  30 158  31 159  32 160  33 161  34 162  35 163  36 164  37 165  38 166  39 167  40 168  41 169  42 170  43 171  44 172  45 173  46 174  47 175  48 176  49 177  50 178  51 179  52 180  53 181  54 182  55 183  56 184  57 185  58 186  59 187  60 188  61 189  62 190  63 191
      Node  1 (1082243698688 bytes mem):  64 192  65 193  66 194  67 195  68 196  69 197  70 198  71 199  72 200  73 201  74 202  75 203  76 204  77 205  78 206  79 207  80 208  81 209  82 210  83 211  84 212  85 213  86 214  87 215  88 216  89 217  90 218  91 219  92 220  93 221  94 222  95 223  96 224  97 225  98 226  99 227 100 228 101 229 102 230 103 231 104 232 105 233 106 234 107 235 108 236 109 237 110 238 111 239 112 240 113 241 114 242 115 243 116 244 117 245 118 246 119 247 120 248 121 249 122 250 123 251 124 252 125 253 126 254 127 255
      Latency:
               0     1
         0  1.00  3.20
         1  3.20  1.00
    Caches:
      L1: 32768 bytes, linesize 64 bytes, assoc. 8, shared 2 ways
      L2: 524288 bytes, linesize 64 bytes, assoc. 8, shared 2 ways
      L3: 33554432 bytes, linesize 64 bytes, assoc. 16, shared 16 ways
    PCI devices:
      0000:41:00.0  Id: 15b3:101d  Class: 0x0200  Numa: 0
      0000:41:00.1  Id: 15b3:101d  Class: 0x0200  Numa: 0
      0000:62:00.0  Id: 102b:0522  Class: 0x0300  Numa: 0

Highest SIMD level requested by all nodes in run: AVX2_256
SIMD instructions selected at compile time:       SSE2
This program was compiled for different hardware than you are running on,
which could influence performance.

The current CPU can measure timings more accurately than the code in
gmx mdrun was configured to use. This might affect your simulation
speed as accurate timings are needed for load-balancing.
Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E.
Lindahl
GROMACS: High performance molecular simulations through multi-level
parallelism from laptops to supercomputers
SoftwareX 1 (2015) pp. 19-25
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
S. Páll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl
Tackling Exascale Software Challenges in Molecular Dynamics Simulations with
GROMACS
In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale 8759 (2015) pp. 3-27
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R.
Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl
GROMACS 4.5: a high-throughput and highly parallel open source molecular
simulation toolkit
Bioinformatics 29 (2013) pp. 845-54
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 435-447
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
Berendsen
GROMACS: Fast, Flexible and Free
J. Comp. Chem. 26 (2005) pp. 1701-1719
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
E. Lindahl and B. Hess and D. van der Spoel
GROMACS 3.0: A package for molecular simulation and trajectory analysis
J. Mol. Mod. 7 (2001) pp. 306-317
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
H. J. C. Berendsen, D. van der Spoel and R. van Drunen
GROMACS: A message-passing parallel molecular dynamics implementation
Comp. Phys. Comm. 91 (1995) pp. 43-56
-------- -------- --- Thank You --- -------- --------


++++ PLEASE CITE THE DOI FOR THIS VERSION OF GROMACS ++++
https://doi.org/10.5281/zenodo.3685922
-------- -------- --- Thank You --- -------- --------

Input Parameters:
   integrator                     = md
   tinit                          = 0
   dt                             = 0.002
   nsteps                         = 50050000
   init-step                      = 0
   simulation-part                = 1
   comm-mode                      = Linear
   nstcomm                        = 100
   bd-fric                        = 0
   ld-seed                        = 1499064193
   emtol                          = 10
   emstep                         = 0.01
   niter                          = 20
   fcstep                         = 0
   nstcgsteep                     = 1000
   nbfgscorr                      = 10
   rtpi                           = 0.05
   nstxout                        = 0
   nstvout                        = 0
   nstfout                        = 0
   nstlog                         = 5000
   nstcalcenergy                  = 100
   nstenergy                      = 5000
   nstxout-compressed             = 5000
   compressed-x-precision         = 1000
   cutoff-scheme                  = Verlet
   nstlist                        = 10
   ns-type                        = Grid
   pbc                            = xyz
   periodic-molecules             = false
   verlet-buffer-tolerance        = 0.005
   rlist                          = 1
   coulombtype                    = PME
   coulomb-modifier               = Potential-shift
   rcoulomb-switch                = 0
   rcoulomb                       = 1
   epsilon-r                      = 1
   epsilon-rf                     = inf
   vdw-type                       = Cut-off
   vdw-modifier                   = Potential-shift
   rvdw-switch                    = 0
   rvdw                           = 1
   DispCorr                       = EnerPres
   table-extension                = 1
   fourierspacing                 = 0.16
   fourier-nx                     = 84
   fourier-ny                     = 84
   fourier-nz                     = 84
   pme-order                      = 4
   ewald-rtol                     = 1e-05
   ewald-rtol-lj                  = 0.001
   lj-pme-comb-rule               = Geometric
   ewald-geometry                 = 0
   epsilon-surface                = 0
   tcoupl                         = V-rescale
   nsttcouple                     = 10
   nh-chain-length                = 0
   print-nose-hoover-chain-variables = false
   pcoupl                         = Parrinello-Rahman
   pcoupltype                     = Isotropic
   nstpcouple                     = 10
   tau-p                          = 2
   compressibility (3x3):
      compressibility[    0]={ 4.50000e-05,  0.00000e+00,  0.00000e+00}
      compressibility[    1]={ 0.00000e+00,  4.50000e-05,  0.00000e+00}
      compressibility[    2]={ 0.00000e+00,  0.00000e+00,  4.50000e-05}
   ref-p (3x3):
      ref-p[    0]={ 1.00000e+00,  0.00000e+00,  0.00000e+00}
      ref-p[    1]={ 0.00000e+00,  1.00000e+00,  0.00000e+00}
      ref-p[    2]={ 0.00000e+00,  0.00000e+00,  1.00000e+00}
   refcoord-scaling               = No
   posres-com (3):
      posres-com[0]= 0.00000e+00
      posres-com[1]= 0.00000e+00
      posres-com[2]= 0.00000e+00
   posres-comB (3):
      posres-comB[0]= 0.00000e+00
      posres-comB[1]= 0.00000e+00
      posres-comB[2]= 0.00000e+00
   QMMM                           = false
   QMconstraints                  = 0
   QMMMscheme                     = 0
   MMChargeScaleFactor            = 1
qm-opts:
   ngQM                           = 0
   constraint-algorithm           = Lincs
   continuation                   = true
   Shake-SOR                      = false
   shake-tol                      = 0.0001
   lincs-order                    = 4
   lincs-iter                     = 1
   lincs-warnangle                = 30
   nwall                          = 0
   wall-type                      = 9-3
   wall-r-linpot                  = -1
   wall-atomtype[0]               = -1
   wall-atomtype[1]               = -1
   wall-density[0]                = 0
   wall-density[1]                = 0
   wall-ewald-zfac                = 3
   pull                           = false
   awh                            = false
   rotation                       = false
   interactiveMD                  = false
   disre                          = No
   disre-weighting                = Conservative
   disre-mixed                    = false
   dr-fc                          = 1000
   dr-tau                         = 0
   nstdisreout                    = 100
   orire-fc                       = 0
   orire-tau                      = 0
   nstorireout                    = 100
   free-energy                    = no
   cos-acceleration               = 0
   deform (3x3):
      deform[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      deform[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      deform[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   simulated-tempering            = false
   swapcoords                     = no
   userint1                       = 0
   userint2                       = 0
   userint3                       = 0
   userint4                       = 0
   userreal1                      = 0
   userreal2                      = 0
   userreal3                      = 0
   userreal4                      = 0
   applied-forces:
     electric-field:
       x:
         E0                       = 0
         omega                    = 0
         t0                       = 0
         sigma                    = 0
       y:
         E0                       = 0
         omega                    = 0
         t0                       = 0
         sigma                    = 0
       z:
         E0                       = 0
         omega                    = 0
         t0                       = 0
         sigma                    = 0
grpopts:
   nrdf:     22331.8      300933
   ref-t:         313         313
   tau-t:         0.1         0.1
annealing:          No          No
annealing-npoints:           0           0
   acc:	           0           0           0
   nfreeze:           N           N           N
   energygrp-flags[  0]: 0


Reading checkpoint file md_0_10.cpt
  file generated by:     /usr/bin/gmx
  file generated at:     Sun Jan 22 08:22:59 2023

  GROMACS double prec.:  0
  simulation part #:     1
  step:                  50000000
  time:                  100000.000000

Changing nstlist from 10 to 50, rlist from 1 to 1.114


Initializing Domain Decomposition on 256 ranks
Dynamic load balancing: locked
Using update groups, nr 54659, average size 2.9 atoms, max. radius 0.139 nm
Minimum cell size due to atom displacement: 0.417 nm
Initial maximum distances in bonded interactions:
    two-body bonded interactions: 0.464 nm, LJ-14, atoms 7842 8658
  multi-body bonded interactions: 0.495 nm, CMAP Dih., atoms 3412 3425
Minimum cell size due to bonded interactions: 0.545 nm
Guess for relative PME load: 0.13
Will use 192 particle-particle and 64 PME only ranks
This is a guess, check the performance at the end of the log file
Using 64 separate PME ranks, as guessed by mdrun
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 192 cells with a minimum initial size of 0.681 nm
The maximum allowed number of cells is: X 15 Y 15 Z 13
Domain decomposition grid 8 x 8 x 3, separate PME ranks 64
PME domain decomposition: 8 x 8 x 1
Interleaving PP and PME ranks
This rank does only particle-particle work.
Domain decomposition rank 0, coordinates 0 0 0

The initial number of communication pulses is: X 2 Y 2 Z 1
The initial domain decomposition cell size is: X 1.35 nm Y 1.35 nm Z 3.11 nm

The maximum allowed distance for atom groups involved in interactions is:
                 non-bonded interactions           1.392 nm
(the following are initial values, they could change due to box deformation)
            two-body bonded interactions  (-rdd)   1.392 nm
          multi-body bonded interactions  (-rdd)   1.348 nm

When dynamic load balancing gets turned on, these settings will change to:
The maximum number of communication pulses is: X 2 Y 2 Z 2
The minimum size for domain decomposition cells is 0.922 nm
The requested allowed shrink of DD cells (option -dds) is: 0.80
The allowed shrink of domain decomposition cells is: X 0.68 Y 0.68 Z 0.30
The maximum allowed distance for atom groups involved in interactions is:
                 non-bonded interactions           1.392 nm
            two-body bonded interactions  (-rdd)   1.392 nm
          multi-body bonded interactions  (-rdd)   0.922 nm

Using 256 MPI threads
Using 1 OpenMP thread per tMPI thread

Pinning threads with an auto-selected logical core stride of 1
System total charge: 0.000
Will do PME sum in reciprocal space for electrostatic interactions.

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen 
A smooth particle mesh Ewald method
J. Chem. Phys. 103 (1995) pp. 8577-8592
-------- -------- --- Thank You --- -------- --------

Using a Gaussian width (1/beta) of 0.320163 nm for Ewald
Potential shift: LJ r^-12: -1.000e+00 r^-6: -1.000e+00, Ewald -1.000e-05
Initialized non-bonded Ewald correction tables, spacing: 9.33e-04 size: 1073

Long Range LJ corr.: <C6> 3.1602e-04
Generated table with 1056 data points for Ewald.
Tabscale = 500 points/nm
Generated table with 1056 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 1056 data points for LJ12.
Tabscale = 500 points/nm
Generated table with 1056 data points for 1-4 COUL.
Tabscale = 500 points/nm
Generated table with 1056 data points for 1-4 LJ6.
Tabscale = 500 points/nm
Generated table with 1056 data points for 1-4 LJ12.
Tabscale = 500 points/nm

Using SIMD 4x4 nonbonded short-range kernels

Using a dual 4x4 pair-list setup updated with dynamic pruning:
  outer list: updated every 50 steps, buffer 0.114 nm, rlist 1.114 nm
  inner list: updated every 12 steps, buffer 0.002 nm, rlist 1.002 nm
At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be:
  outer list: updated every 50 steps, buffer 0.244 nm, rlist 1.244 nm
  inner list: updated every 12 steps, buffer 0.048 nm, rlist 1.048 nm

Using Lorentz-Berthelot Lennard-Jones combination rule


Initializing LINear Constraint Solver

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije
LINCS: A Linear Constraint Solver for molecular simulations
J. Comp. Chem. 18 (1997) pp. 1463-1472
-------- -------- --- Thank You --- -------- --------

The number of constraints is 4413

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
S. Miyamoto and P. A. Kollman
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
Water Models
J. Comp. Chem. 13 (1992) pp. 952-962
-------- -------- --- Thank You --- -------- --------


Linking all bonded interactions to atoms


Intra-simulation communication will occur every 10 steps.
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
  0:  rest

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
G. Bussi, D. Donadio and M. Parrinello
Canonical sampling through velocity rescaling
J. Chem. Phys. 126 (2007) pp. 014101
-------- -------- --- Thank You --- -------- --------

There are: 159382 Atoms
Atom distribution over 192 domains: av 830 stddev 27 min 780 max 921

Started mdrun on rank 0 Thu Jan 26 11:49:07 2023

           Step           Time
       50000000   100000.00000

   Energies (kJ/mol)
           Bond            U-B    Proper Dih.  Improper Dih.      CMAP Dih.
    7.34629e+03    2.05344e+04    1.38964e+04    1.23015e+03   -3.39566e+03
          LJ-14     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)
    6.00855e+03    1.11361e+05    3.37467e+05   -2.05968e+04   -2.58784e+06
   Coul. recip.      Potential    Kinetic En.   Total Energy  Conserved En.
    1.44623e+04   -2.09953e+06    4.20164e+05   -1.67936e+06    3.48355e+06
    Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
    3.12648e+02   -2.10004e+02   -1.08826e+02    4.23227e-06


DD  step 50000049 load imb.: force 18.2%  pme mesh/force 1.568

step 50000150 Turning on dynamic load balancing, because the performance loss due to load imbalance is 9.7 %.


Received the INT signal, stopping within 50 steps

           Step           Time
       50004200   100008.40000

Writing checkpoint, step 50004200 at Thu Jan 26 11:49:16 2023


   Energies (kJ/mol)
           Bond            U-B    Proper Dih.  Improper Dih.      CMAP Dih.
    7.38078e+03    2.07505e+04    1.38326e+04    1.34316e+03   -3.35548e+03
          LJ-14     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)
    6.11282e+03    1.11841e+05    3.38614e+05   -2.05940e+04   -2.58776e+06
   Coul. recip.      Potential    Kinetic En.   Total Energy  Conserved En.
    1.48792e+04   -2.09696e+06    4.22257e+05   -1.67470e+06    3.48402e+06
    Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
    3.14206e+02   -2.09948e+02    3.87643e+01    4.16659e-06

	<======  ###############  ==>
	<====  A V E R A G E S  ====>
	<==  ###############  ======>

	Statistics over 4201 steps using 43 frames

   Energies (kJ/mol)
           Bond            U-B    Proper Dih.  Improper Dih.      CMAP Dih.
    7.40247e+03    2.05473e+04    1.38797e+04    1.25636e+03   -3.35615e+03
          LJ-14     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)
    6.05382e+03    1.12012e+05    3.39178e+05   -2.05937e+04   -2.58862e+06
   Coul. recip.      Potential    Kinetic En.   Total Energy  Conserved En.
    1.45791e+04   -2.09767e+06    4.20693e+05   -1.67697e+06    3.48380e+06
    Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
    3.13042e+02   -2.09941e+02   -6.79831e+00    0.00000e+00

          Box-X          Box-Y          Box-Z
    1.32123e+01    1.32123e+01    9.34248e+00

   Total Virial (kJ/mol)
    1.40248e+05   -1.00274e+02   -4.18899e+02
   -8.37406e+01    1.40581e+05   -2.09403e+02
   -4.18510e+02   -2.27405e+02    1.40872e+05

   Pressure (bar)
    1.38813e+00    5.17630e+00    7.16666e+00
    4.83939e+00   -7.94230e+00    5.37324e+00
    7.15851e+00    5.73972e+00   -1.38408e+01

      T-Protein  T-non-Protein
    3.13608e+02    3.13000e+02


	M E G A - F L O P S   A C C O U N T I N G

 NB=Group-cutoff nonbonded kernels    NxN=N-by-N cluster Verlet kernels
 RF=Reaction-Field  VdW=Van der Waals  QSTab=quadratic-spline table
 W3=SPC/TIP3p  W4=TIP4p (single or pairs)
 V&F=Potential and force  V=Potential only  F=Force only

 Computing:                               M-Number         M-Flops  % Flops
-----------------------------------------------------------------------------
 Pair Search distance check            6390.268962       57512.421     0.4
 NxN QSTab Elec. + LJ [F]            199069.098504     8161833.039    51.5
 NxN QSTab Elec. + LJ [V&F]            2058.675896      121461.878     0.8
 NxN LJ [F]                              23.305360         769.077     0.0
 NxN LJ [V&F]                             0.229552           9.871     0.0
 NxN QSTab Elec. [F]                 179379.719016     6098910.447    38.5
 NxN QSTab Elec. [V&F]                 1854.999432       76054.977     0.5
 1,4 nonbonded interactions              98.828525        8894.567     0.1
 Calc Weights                          2008.691346       72312.888     0.5
 Spread Q Bspline                     42852.082048       85704.164     0.5
 Gather F Bspline                     42852.082048      257112.492     1.6
 3D-FFT                               95499.282912      763994.263     4.8
 Solve PME                              237.138048       15176.835     0.1
 Reset In Box                            13.388088          40.164     0.0
 CG-CoM                                  13.547470          40.642     0.0
 Bonds                                   19.354007        1141.886     0.0
 Propers                                 83.763739       19181.896     0.1
 Impropers                                6.230083        1295.857     0.0
 Virial                                  70.737262        1273.271     0.0
 Stop-CM                                  6.853426          68.534     0.0
 Calc-Ekin                              134.199644        3623.390     0.0
 Lincs                                   18.539013        1112.341     0.0
 Lincs-Mat                               95.581152         382.325     0.0
 Constraint-V                           669.181491        5353.452     0.0
 Constraint-Vir                          65.203638        1564.887     0.0
 Settle                                 210.701155       68056.473     0.4
 CMAP                                     2.449183        4163.611     0.0
 Urey-Bradley                            68.358672       12509.637     0.1
-----------------------------------------------------------------------------
 Total                                                15839555.286   100.0
-----------------------------------------------------------------------------


    D O M A I N   D E C O M P O S I T I O N   S T A T I S T I C S

 av. #atoms communicated per step for force:  2 x 612439.6


Dynamic load balancing report:
 DLB was turned on during the run due to measured imbalance.
 Average load imbalance: 6.5%.
 The balanceable part of the MD step is 81%, load imbalance is computed from this.
 Part of the total run time spent waiting due to load imbalance: 5.3%.
 Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % Y 0 % Z 0 %
 Average PME mesh/force load: 0.649
 Part of the total run time spent waiting due to PP/PME imbalance: 7.6 %

NOTE: 5.3 % of the available CPU time was lost due to load imbalance
      in the domain decomposition.
      You can consider manually changing the decomposition (option -dd);
      e.g. by using fewer domains along the box dimension in which there is
      considerable inhomogeneity in the simulated system.
NOTE: 7.6 % performance was lost because the PME ranks
      had less work to do than the PP ranks.
      You might want to decrease the number of PME ranks
      or decrease the cut-off and the grid spacing.


     R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G

On 192 MPI ranks doing PP, and
on 64 MPI ranks doing PME

 Computing:          Num   Num      Call    Wall time         Giga-Cycles
                     Ranks Threads  Count      (s)         total sum    %
-----------------------------------------------------------------------------
 Domain decomp.       192    1         84       0.168         78.833   1.3
 DD comm. load        192    1         84       0.001          0.481   0.0
 DD comm. bounds      192    1         82       0.007          3.333   0.1
 Send X to PME        192    1       4201       0.031         14.747   0.3
 Neighbor search      192    1         85       0.514        241.315   4.1
 Comm. coord.         192    1       4116       0.482        226.252   3.9
 Force                192    1       4201       6.776       3180.570  54.3
 Wait + Comm. F       192    1       4201       0.808        379.231   6.5
 PME mesh *            64    1       4201       4.848        758.608  13.0
 PME wait for PP *                              4.503        704.530  12.0
 Wait + Recv. PME F   192    1       4201       0.037         17.569   0.3
 NB X/F buffer ops.   192    1      12433       0.157         73.769   1.3
 Write traj.          192    1          2       0.029         13.836   0.2
 Update               192    1       4201       0.033         15.567   0.3
 Constraints          192    1       4201       0.076         35.677   0.6
 Comm. energies       192    1        421       0.188         88.293   1.5
 Rest                                           0.045         21.344   0.4
-----------------------------------------------------------------------------
 Total                                          9.354       5854.423 100.0
-----------------------------------------------------------------------------
(*) Note that with separate PME ranks, the walltime column actually sums to
    twice the total reported, but the cycle count total and % are correct.
-----------------------------------------------------------------------------
 Breakdown of PME mesh computation
-----------------------------------------------------------------------------
 PME redist. X/F       64    1       8402       1.105        172.869   3.0
 PME spread            64    1       4201       1.011        158.142   2.7
 PME gather            64    1       4201       1.063        166.329   2.8
 PME 3D-FFT            64    1       8402       1.036        162.065   2.8
 PME 3D-FFT Comm.      64    1      16804       0.452         70.716   1.2
 PME solve Elec        64    1       4201       0.175         27.341   0.5
-----------------------------------------------------------------------------

               Core t (s)   Wall t (s)        (%)
       Time:     2394.033        9.354    25593.4
                 (ns/day)    (hour/ns)
Performance:       77.606        0.309
Finished mdrun on rank 0 Thu Jan 26 11:49:16 2023

